# Genomic Coordinates

Convert genomic intervals between coordinate conventions, normalise and compare variant...

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-10-30
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill genomic-coordinates -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill genomic-coordinates -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill genomic-coordinates -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill genomic-coordinates -g -a gemini-cli -y`

## Description

Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Genomic Coordinates

## When to use

Any time a coordinate crosses a boundary: between two file formats, between two
tools, between two assemblies, or between the genome and a transcript.

## The rule

**A coordinate is three facts, not one: the number, the convention it is written
in, and the assembly it was measured against.** Carry all three or the number is
not interpretable.

Coordinate errors are the quietest class of bug in genomics. An off-by-one BED
file parses, sorts, and intersects without complaint. A GRCh37 VCF joined against
a GRCh38 annotation returns rows. A right-shifted indel simply fails to match its
entry in ClinVar, and the result is a variant reported as novel. Nothing raises
an error; the answer is just wrong, and it is wrong in a direction that looks
plausible.

So: convert with the table, not from memory, and verify against the reference
whenever a reference is available.

## The two conversions

```
1-based inclusive  ->  0-based half-open :  start - 1,  end
0-based half-open  ->  1-based inclusive :  start + 1,  end
```

The end coordinate never moves. If a conversion changed both numbers, it is wrong.

## Which format is which

| 0-based, half-open | 1-based, inclusive |
| --- | --- |
| BED, bedGraph, bigWig, narrowPeak | GFF3, GTF, VCF |
| BAM/CRAM (binary POS) | SAM (text POS) |
| PSL, genePred, refFlat | WIG, Picard interval_list |
| MAF (UCSC multiple alignment) | MAF (TCGA mutation annotation) |
| PyRanges, pybedtools | GRanges/IRanges, samtools & UCSC & Ensembl region strings |

Both "MAF" formats exist, they mean different things, and they disagree. UCSC
serves 0-based files through a 1-based browser box. `references/format-conventions.md`
has the full table with per-format detail.

```bash
cd skills/genomic-coordinates/scripts

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/genomic-coordinates/SKILL.md